• Volume 9, 2019
  • Volume 8, 2018
  • Volume 7, 2017
  • Volume 6, 2016
  • Volume 5, 2015
  • Volume 4, 2014
  • Volume 3, 2013
  • Volume 2, 2012
  • Volume 1, 2011

Cancer Biology

DNA in situ Hybridizations for VEGFA Gene Locus (6p12) in Human Tumor Tissue Authors:  Mariacarla Andreozzi, Luca Quagliata, Katharina Burmeister, Leila Arabi, Sandra Schneider, Luigi Tornillo and Luigi Terracciano, date: 08/05/2015, view: 5455, Q&A: 0
Over the last decades numerous regulators of angiogenesis have been identified and characterized. Among the others the vascular endothelial growth factor (VEGFA) appears undoubtedly important in several pathophysiological processes. Moreover, VEGFA represents one of the most attractive targets of anticancer therapy, given its major role in the ...
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Cell Biology

Assessing Mitochondrial Transport via Cytoplasmic Nanotubular Bridges in Cells Authors:  Shravani Mukherjee, Tanveer Ahmad and Anurag Agrawal, date: 08/05/2015, view: 4905, Q&A: 0
This protocol aims to study intercellular transport of mitochondria, dynamic cellular organelles via tunnelling nanotubes (TNT), a cell membrane extension of cytoskeletal elements. The nanotubular bridges or the tunnelling nanotube highways are one of the emerging new cell-to-cell communication systems which mediates exchange of cellular ...
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Developmental Biology

Mouse Retinal Whole Mounts and Quantification of Vasculature Protocol Authors:  Irit Adini and Kaustabh Ghosh, date: 08/05/2015, view: 9439, Q&A: 0
Angiogenesis is the formation of new blood vessels from a pre-existing vascular bed. It is a multi-step process beginning with enzymatic degradation of the capillary basement membrane, followed by endothelial cell (EC) proliferation, migration, tube formation, assembly of a new basement membrane, and pericyte stabilization. Aberrant angiogenesis ...
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Quantification of ex vivo Neutrophil Extracellular Traps Authors:  Koji Tanaka, Masato Okigami, Yuji Toiyama, Yoshinaga Okugawa, Yasuhiro Inoue, Toshimitsu Araki, Yasuhiko Mohri, Akira Mizoguchi and Masato Kusunoki, date: 08/05/2015, view: 6559, Q&A: 0
Neutrophil extracellular traps (NETs) are fibrous mesh-like, web-like, or string-like structures which are composed of DNA, histones, and granule proteins such as neutrophil elastase or myeloperoxidase. When activated by phorbol myristate acetate, interleukin-8, lipopolysaccharide (LPS), and various pathogens, neutrophils release NETs. We reported ...
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Visualization of ex vivo Neutrophil Extracellular Traps by Fluorescence Microscopy Authors:  Koji Tanaka, Tadanobu Shimura, Yuji Toiyama, Yoshinaga Okugawa, Yasuhiro Inoue, Toshimitsu Araki, Yasuhiko Mohri, Akira Mizoguchi and Masato Kusunoki, date: 08/05/2015, view: 6690, Q&A: 0
Neutrophil extracellular traps (NETs) are extracellular DNAs decorated with nuclear and granular proteins such as histones, neutrophil elastase or myeloperoxidase. They exhibit fibrous mesh-like, web-like, or string-like structures. Here, we describe our protocol regarding visualization of ex vivo NETs released from neutrophils activated ...
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XTT Assay of Antifungal Activity Authors:  Flávio V. Loures and Stuart M. Levitz, date: 08/05/2015, view: 5825, Q&A: 0
XTT assay is a colorimetric method that uses the tetrazolium dye, 2,3-bis-(2-methoxy-4-nitro-5-sulphenyl)-(2H)-tetrazolium-5-carboxanilide (XTT) to quantify cell-mediated damage to fungi. Actively respiring fungal cells convert the water-soluble XTT to a water-soluble, orange colored formazan product (Meshulam et al., 1995). Here, we ...
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Detection of HBV C Protein Phosphorylation in the Cell Authors:  Jaesung Jung and Kyongmin Kim, date: 08/05/2015, view: 4861, Q&A: 0
Among the seven serines and one threonine in the carboxyl-terminus of HBV C protein, all but one (serine 183) appear in the context of RxxS/T consensus phosphoacceptor motifs and also overlap with other consensus motifs, such as S/TP, RS, SPRRR, RRRS/T, or RRxS/T, suggesting that various cellular kinases phosphorylate these residues. To determine ...
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Primer Extension Analysis of HBV DNA with Strand-Specific Primers Authors:  Jaesung Jung and Kyongmin Kim, date: 08/05/2015, view: 4680, Q&A: 0
We performed primer extension assay to determine which steps of HBV DNA synthesis (i.e., minus- and plus-strand DNA synthesis and circularization of RC DNA) are affected by phosphoacceptor site mutations in C protein. In these experiments, we used several specific oligonucleotide primers. For quantitation, the level of extended DNA (ED) ...
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Evaluation of Nodulation Speed by Sinorhizobium Strains Authors:  Matthew S. Nelson, Chan Lan Chun and Michael J. Sadowksy, date: 08/05/2015, view: 5147, Q&A: 0
Rhizobia interact symbiotically with legumes to form root nodules, where by rhizobia fix atmospheric dinitrogen into ammonia in exchange for carbon produced via photosynthesis. The symbiotic interaction is agriculturally important by reducing the need for fertilizer containing nitrogen. The root and stem nodule bacteria commonly include bacteria ...
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Quantitative Evaluation of Competitive Nodulation among Different Sinorhizobium Strains Authors:  Chan Lan Chun, Matthew S. Nelson and Michael J. Sadowksy, date: 08/05/2015, view: 4461, Q&A: 0
Legumes play a vital role in global food supply because they are uniquely capable of fixing atmospheric nitrogen (N) through symbioses with root and stem nodule bacteria, collectively called the rhizobia. These commonly include bacteria in the genera Rhizobium, Mesorhizobium, Sinorhizobium (Ensifer), and Bradyrhizobium ...
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Measuring Blood-brain-barrier Permeability Using Evans Blue in Mice Authors:  Jun-Xia Yang, Yan-Yu Jiang and Yu-Bai Guo, date: 08/05/2015, view: 12636, Q&A: 1
The blood–brain barrier (BBB) is a highly selective permeability barrier that separates the circulating blood from the brain extracellular fluid in the central nervous system. The blood–brain barrier allows the passage of water, some gases, and lipid soluble molecules by passive diffusion, as well as the selective transport of molecules such as ...
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Plant Science

Expression and Purification of the Arabidopsis E4 SUMO Ligases PIAL1 and PIAL2 Authors:  Konstantin Tomanov and Andreas Bachmair, date: 08/05/2015, view: 4154, Q&A: 0
The proteins PIAL1 (At1g08910) and PIAL2 (At5g41580) are members of the recently discovered group of plant E4 SUMO ligases. This protocol allows quick and simple expression of the recombinant proteins in Escherichia coli (E. coli) and subsequent affinity purification using a maltose binding protein (MBP) tag. The proteins can be ...
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Genomic DNA Extraction and Genotyping of Dictyochloropsis Green Algae Strains Authors:  Francesco Dal Grande, Carolina Cornejo, Christoph Scheidegger and Andreas Beck, date: 08/05/2015, view: 7429, Q&A: 0
Dictyochloropsis is an ecologically important genus of free-living and symbiotic green algae. Representatives of this genus are horizontally transmitted among several fungi of the family Lobariaceae, thus forming photobiont-mediated guilds. This protocol is suitable for extracting DNA from algal cultures and lichen samples and for ...
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Tissue Culturing and Harvesting of Protonemata from the Moss Physcomitrella patens Authors:  Xiaoqin Wang and Yikun He, date: 08/05/2015, view: 5456, Q&A: 0
Moss spores germinate to form an alga-like filamentous structure called the protonemata. Protonemata are the earliest stage (the haploid phase) of a bryophyte life cycle and eventually give rise to a mature gametophyte. Protonemata of the moss Physcomitrella patens (P. patens) are important not only in their life cycle, but also ...
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Systems Biology

Protocol for the Generation of a Transcription Factor Open Reading Frame Collection (TFome) Authors:  John Gray, Brett Burdo, Mary P. Goetting-Minesky, Bettina Wittler, Matthew Hunt, Tai Li, David Velliquette, Julie Thomas, Tina Agarwal, Kasey Key, Irene Gentzel, Michael dos Santos Brito, Maria Katherine Mejía-Guerra, Layne N. Connolly, Dalya Qaisi, Wei Li, Maria I. Casas, Andrea I. Doseff and Erich Grotewold, date: 08/05/2015, view: 7745, Q&A: 1
The construction of a physical collection of open reading frames (ORFeomes) for genes of any model organism is a useful tool for the exploration of gene function, gene regulation, and protein-protein interaction. Here we describe in detail a protocol that has been used to develop the first collection of transcription factor (TF) and co-regulator ...
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